So here's my complex little situation.
Over the past year I've noticed my pedal going soft. I figured it would be the master cylinder, so this fall I replaced the unit with a new one from NAPA. Bench bled, intstalled, bled the system. However, at the time, I couldn't bleed the ABS system fully. After I replaced the master cylinder, my ABS light started coming on. When I would start the car, my ABS pump would come on and run constantly for 1-2 minutes, then stop and the ABS light would come on every time. Stupid me didn't pull the code at the time.

So I drove it around for a couple weeks, re-bleeding the ABS once or twice a week. Each time I would get some air, but not all of it. After several months and not really any progress, I took it into my mechanic. He pressure bled the system and inspected the rest of it. After he bled it, the ABS light went off, but the pedal was still soft.
So....he thought it may be a faulty master cylinder. So we replaced it with another one.... and then a third... no luck. Same feeling in the pedal.
He tried calling he Honda dealer (which is 90 miles away) and they were absolutely no help. They want me to take the car to them (obviously because they want my $$$, but I can't see driving it 90 miles with the brakes almost non-functional.) Since the ABS light is no longer on, I don't know what good they can do that my mechanic cannot.

The opinion of my mechanic is that the ABS modulator assembly is likely the culprit. Or possibly the control modulator. Either way, I'm not replacing them with new ones from Honda, I'll find used if I need to.

Any ideas or suggestions as to what's going on and how to fix it?

 

I don't think the ABS unit is causing the spongyness of your brake pedal. ABS only controls the mechanism when your car is sliding. It does nothing during normal braking.

If you can brake only when the pedal almost touching the floor, it may mean your front brake is nonfunctional. Only the rear brakes are working. It still points to the master cylinder.

If your pedal rises after you pump it, it means you got air in the system. Bleed them according to Honda's reco, FL, FR, RR, RL.

 

well I've gone through 3 brand new master cylinders and manually bled the system 4 times and had it pressure bled once and nothing has helped.... So I'm pretty sure it isn't the MC

 

If the replacement master cylinder isn't OEM or 'Adler' there is a possibility that the brake push rod needs to be adjusted.
Don't adjust more than 1/4 turn at a time and then test drive, it's not cool if you adjust it too far and the brakes hang up and drag all the time.
Honda has a special jig that mounts to the brake booster and then the brake push rod is adjusted to that certain "special" setting.